I would clean it up before using another smoothing modifier. Then after you the smooth the mesh, clean it up again. Look for areas that have geometry that isn't being used to define anything. Pretty much every vertex should describe a change in the shape.
When I make my models, I make an extremely blocky version, to get the shape right. I spend quite a while on it, and it doesn't have many polygons in it (<500, like). No triangles, however. I save a copy, and that will become LODx in the future. Then apply my smooth modifier.
Then I clean it up again. Rounded parts keep their extra detail, flat areas lose them. At this point I'm still avoiding triangles. Here I'll start adding the more subtle changes in shape that couldn't be describe in the pre-smooth version.
After that, I smooth it again. Then I clean it up, this time introducing triangles wherever they won't screw with smoothing too much. Mostly flat areas. Then I move on to turrets and greebles and whatever.
I'm not really a detail-phile, so most of my finished models don't exceed 25 000 polygons. I'm a gestalt kind of guy, more interested in the overall shape rather than finicky details, so my taste may differ than yours. I guess I would caution against adding polygons just for the sake of adding polygons.